COMMENTARY a Chromomeric Model for Nuclear and Chromosome Structure
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Journal of Cell Science 108, 2927-2935 (1995) 2927 Printed in Great Britain © The Company of Biologists Limited 1995 COMMENTARY A chromomeric model for nuclear and chromosome structure Peter R. Cook CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK e-mail: [email protected] SUMMARY The basic structural elements of chromatin and chromo- into mitosis, increased adhesiveness between nucleosomes somes are reviewed. Then a model involving only three and between factories drives a ‘sticky-end’ aggregation to architectural motifs, nucleosomes, chromatin loops and the most compact and stable structure, a cylinder of nucle- transcription factories/chromomeres, is presented. Loops osomes around an axial chromomeric core. are tied through transcription factors and RNA poly- merases to factories during interphase and to the remnants of those factories, chromomeres, during mitosis. On entry Key words: chromomere, nucleoskeleton, RNA polymerase, factory INTRODUCTION meric model will be presented; it helps explain how the inter- phase fibre is converted into a mitotic chromosome and why a ‘We are thus brought, finally, to one of the most fundamental chromosome has its characteristic shape. conceptions of cytology and genetics, namely, that the A number of inter-related factors complicate analysis of spireme-threads are linear aggregates of much smaller self-per- chromosome structure. First, their tight packing and high petuating bodies, aligned in single series, and in definite order.’ density makes it difficult to visualize their interior and limits As chromosomes condense, these bodies, or chromomeres, access of probes like antibodies. Second, chromatin is poised may ‘aggregate or fuse to form larger ones’ and ‘be compound in a metastable state so that even small changes in tonicity bodies having perhaps a definite internal architecture.’ cause it to aggregate into an unworkable mess. Therefore These quotations are taken from the concluding section on unphysiological conditions are used in almost all isolation pro- chromosome structure in E. B. Wilson’s classic review of cell cedures; for example, conventional cytological preparations biology published in 1928 (Wilson, 1928); they summarize a are made by hypotonically swelling cells, followed by half-century of careful microscopic analyses of chromosomes fixation/extraction in methanol-acetic acid and an explosive of many different organisms. Strings of chromomeres were spreading at an air-liquid interface. Third, chromosomal sub- traced from interphase as they condensed, split and segregated structures have sizes below the resolution of the light micro- during mitosis, to decondense in the daughter cells. Whilst the scope, necessitating electron microscopy which brings compound term spireme-thread (spirema: a thing wound or problems associated with preserving structure in vacuo. coiled, a skein) expresses an ambivalence as to whether the Therefore, studies on isolates made using more physiological string condensed spirally, the reader is left in no doubt that conditions or on rapidly-frozen specimens will be stressed. chromosomes are built around chromomeres. Despite the wealth of evidence available to Wilson, chro- momeric models fell out of favour, largely because they did BASIC FEATURES OF CHROMOSOME not lead to a plausible explanation of why chromosomes have ORGANIZATION the shape that they have. Furthermore, Wilson presumed that some vestige of the chromomere persisted during interphase, Condensation is the hallmark of mitosis. Why, then, does the but no suitable structure could be found. As a result, most chromatin fibre not condense into the most compact form, a current models involve some form of helical coiling or ill- sphere? Why are chromatids cylindrical, and not spherical? defined interactions between DNA and/or proteins to account for chromosome structure (Fig. 1). However, a good candidate Helical hierarchies for the interphase counterpart of the mitotic chromomere has It is a truism that extended biological structures are helical at now been uncovered. Here, the basic structural elements of the molecular level, but not at the macro-molecular level; actin chromatin and chromosomes that any model must take into filaments and DNA are helical, but cells and trees, which are account will first be reviewed and then an up-dated chromo- nevertheless made of those helical molecular assemblies, are 2928 P. R. Cook not. This truism arises because assembly of molecular sub- has, in 1 mM monovalent ion, the canonical ‘beads-on-a- units into a non-helical structure requires that each sub-unit is string’ structure visible by electron microscopy (Thoma et al., positioned next to its neighbours with no axial rotation; even 1979). As the ionic strength is raised progressively, the string the slightest adds up over many sub-units to give a helix. folds into a series of helices with a fairly constant pitch but Therefore we might expect a hierarchy of helices in a chro- increasing numbers of nucleosomes per turn; at ~60 mM, the mosome: the double helix first being coiled into a nucleosome resulting ‘solenoid’ is ~25 nm wide, with 6-8 nucleosomes/turn (~11 nm diam.), nucleosomes into solenoids (~30 nm diam.), and an 11 nm pitch. But both right- and left-handed solenoids solenoids into chromatid fibres (225-250 nm diam.), and so on are seen in the original micrographs, implying some disorder. to give a cylinder (Fig. 1E). At each level in the hierarchy, the Moreover, others interpret rather similar structures in terms of sense of coiling and pitch between monomers would be strings of ‘superbeads’ (Hozier et al., 1977; Strätling et al., precisely defined. According to this view, one might solve (in 1978). Increasing the salt concentration further has little effect a crystallographic sense) the structure of a mitotic chromosome until chromatin precipitates at ~100 mM, so these experiments and expect some remnants of the hierarchy to be retained into provide no direct evidence that solenoids exist at a physiolog- interphase. However, when biological structures become as ically-relevant salt concentration (i.e. ~150 mM monovalent long as cells, they also become sufficiently flexible that other ion). forces, like those involved in growth, can overcome the weaker There is also no evidence for solenoids in vitrified sections forces maintaining helicity. A long disordered structure may of metaphase CHO or HeLa cells that have been neither fixed well relax into a helix when the other forces are removed in nor stained (McDowall et al., 1986). Chromosomes have a vitro, so the crucial question is whether any coiling then seen homogeneous ‘grainy’ texture and optical diffractograms are actually pre-existed in vivo. best explained by a compact association of 11 nm particles There is no reason to believe that the DNA coils seen in interacting in a manner akin to molecules in a liquid. It is nucleosomal crystals do not exist in vivo, but the evidence for unlikely that solenoids did exist but were missed, because coiling at the next level of organization is controversial. microtubules with the same mass/unit-length can be seen in the Chromatin released from nuclei by digestion with a nuclease cytoplasm. Electron tomography of interphase nuclei embedded at low temperatures also reveals ribbons of zig- zagging nucleosomes and not solenoids; variable lengths of linker DNA seem to enter and exit individual nucleosomes at various angles in the disordered structure, instead of the more precise arrangement expected of a solenoid (Horowitz et al., 1994). There is also controversy over the coiling of the chromone- mal fibre (Manton, 1950): gyres can vary with growth tem- perature in Tradescantia (Swanson, 1942), they may appear constant in number but variable in sense in hypotonically- swollen human chromosomes (Ohnuki, 1968), of opposite sense in a minority of the sister chromatids of isolated HeLa ‘scaffolds’ (Boy de la Tour and Laemmli, 1988), or right- handed in polytene Drosophila chromosomes (Hochstrasser and Sedat, 1987). Coupled with the gap in the hierarchy at the level of the solenoid, such variability smacks more of vari- ability in growth rate or in the conditions at the time of analysis than of some general structural principle. Moreover, an attrac- tive feature of coiled-coil models is that progressive rotation can progressively condense the coil, but chromatids condense without rotation; human vimentin genes tend to retain the same external position on sister chromatids, irrespective of chromatid length (Baumgartner et al., 1991). 30 nm fibres Fig. 1. Some models for chromosome structure during G1 phase and mitosis. Possible G1 structures include (A) a randomly-folded fibre, A ~30 nm fibre is widely believed to be another architectural loops attached (B) to the lamina (e.g. Gerace and Burke, 1988), motif but, again, there is little agreement on its precise dimen- (C) to chromomeres (e.g. Zatsepina et al., 1989) or scaffolds (e.g. sions, the amount of DNA/unit-length and its existence in vivo Paulson and Laemmli, 1977), (D) to proteins bound at specific sites (e.g. van Holde, 1988). Recent careful work suggests that a true on the fibre, or (E) a coiled-coil (e.g. Rattner, 1992). After biological variation underlies this controversy (Woodcock, duplicating DNA and dissolving skeletons, mitotic structure might be 1994). It seems that 30 nm fibres are found in transcription- dictated by interactions (F) within randomly-folded chromatids (e.g. ally-inactive cells like chicken erythrocytes with condensed DuPraw 1966), (G) between chromomeres or scaffolding elements chromatin and ‘long’ (i.e. >210 bp) nucleosomal repeats, but (e.g. Manuelidis, 1990), or (H) between gyres that tighten a coiled- coil (e.g. Bak et al., 1977). Hybrid models (not shown) might involve not in active cells with ‘typical’ repeats of 160-200 bp. For coiled-coils and loops attached to a skeleton or combinations of example, 30 nm fibres are clearly seen in frozen-hydrated radial loops and helical folding (e.g.